Tutorial-l Mailing List

From: Basheer Subei (basheersubei_at_gmail.com)
Date: Sun Aug 24 2014 - 16:40:31 CDT

@Jeff
Thanks for your great answer!

So, I take it that as long as I use the same restraint file
(sin_restraint.pdb in this tutorial) not the last-frame equilibrated
coordinate file, there should be no issue, right?

As for the SiN force field, doesn't section 3.6.10 of the tutorial define a
SiN force field specific to DNA (so that DNA interactions are somewhat
accurate)? Hopefully, it will be good enough...

I'll continue on with the tutorial and I'll get back here if I need more
help. Thanks everyone!

On Sat, Aug 23, 2014 at 1:16 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:

> Hi Basheer,
>
> Using the already equilibrated DNA is a good idea. I think the
> tutorial was written so that you could skip some parts and each
> section would be self-contained. But there should be no problem using
> equilibrated DNA, assuming that the force field used doesn't make
> native DNA structures fall apart, which was a problem for older CHARMM
> and Amber force fields
> (http://dx.doi.org/10.1529/biophysj.106.097782).
>
> On the other hand, for the SiN, you should be careful to maintain the
> atomic positions in the original crystal structure when starting from
> an "equilibrated" SiN structure. It might be easy, by mistake, to grab
> the last frame of your equilibration and use this last frame to define
> the positions to which the atoms are restrained. The SiN force field
> is intended to be used with the atoms restrained to the crystal
> structure. Given that the structure is restrained anyway, there might
> not be much of a need to equilibrate SiN.
>
> Note that the SiN force field hasn't been particularly well calibrated
> for many purposes — it was only designed to reproduce the dielectric
> constant of SiN. Binding of ions or DNA may not be accurate. The SiO2
> force field has undergone more testing
> (http://dx.doi.org/10.1021/jp063896o). For SiO2, you need to be
> careful to maintain the restraint positions to the last frame of the
> annealing (where a different force field is used).
>
> Jeffrey Comer, PhD
> Assistant Professor
> Department of Anatomy and Physiology
> Kansas State University
> College of Veterinary Medicine
>
>
> On Sat, Aug 23, 2014 at 12:43 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> > Hi Basheer,
> >
> > Using the already
> >
> > Jeffrey Comer, PhD
> > Assistant Professor
> > Department of Anatomy and Physiology
> > Kansas State University
> > College of Veterinary Medicine
> >
> >
> > On Fri, Aug 22, 2014 at 7:35 PM, Basheer Subei <basheersubei_at_gmail.com>
> wrote:
> >> Hello all,
> >>
> >> In the Nanopore Tutorial (forgive me if this is the wrong mailing
> list), in
> >> section 3.6, the first step is to combine both the SiN nanopore and the
> >> dsDNA by running the script "combine.tcl. However, the script uses the
> >> unequilibrated structures "dsdna.pdb" and "sin_pore_charges.pdb" (i.e.
> >> before minimization and equilibration).
> >>
> >> Is there a reason why the tutorial doesn't just use the
> already-equilibrated
> >> structures from the previous sections 3.1 and 3.3? I just want to make
> sure
> >> that there isn't some reason unknown to me why I can't just use the
> >> equilibrated dsDNA and SiN nanopore and combine them. (of course, I'll
> take
> >> care to remove the water and ions from the DNA before combining it with
> the
> >> nanopore and then minimize and equilibrate the combined system as
> normal)
> >>
> >> Am I on the right track? Thanks in advance!
> >>
> >> - Basheer Subei
>

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